[gmx-users] Re: simulation of protein/water and phosphate ion

[bharat gupta]

Hi,

I tried simulating the system again but this time with 2 phsophate ion and
the charge of the system was neutralized by adding 6 sodium ions . After
minimizing , I equilibrated for 500 ps but I got "LINCS" error around
300ps.  It's happening due to the addition of phosphate ions as I have
simulated my protein in water earlier without any problem. During nvt
quilibration the temperature coupling settings were for Protein and Non
protein groups. Do I have to make groups for Protein and water_ion. Please
comment??

On Tue, Sep 27, 2011 at 7:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> bharat gupta wrote:
>
>> HI,
>>
>> I have tried simulating my protein (GFP) solvated with water molecules and
>> 10 phosphate ions. During the md run step the system starts exploding after
>>  500 ps. What could be the reason for this . I know this is happening due to
>> the addition of phosphate ion but I need to study the binding of ions . So,
>> what shall I do ??
>>
>>
> http://www.gromacs.org/**Documentation/Terminology/**
> Blowing_Up#Diagnosing_an_**Unstable_System<http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
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> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
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E-mail : monu46010 at yahoo.com
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